3PYK | pdb_00003pyk

Human Carbonic Anhydrase II as Host for Pianostool Complexes Bearing a Sulfonamide Anchor

• PDB DOI: https://doi.org/10.2210/pdb3PYK/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-12-13 Released: 2011-07-13 
• Deposition Author(s): Heinisch, T., Schirmer, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.165 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Human Carbonic Anhydrase II as a host for piano-stool complexes bearing a sulfonamide anchor.

Monnard, F.W., Heinisch, T., Nogueira, E.S., Schirmer, T., Ward, T.R.

(2011) Chem Commun (Camb) 47: 8238-8240

• PubMed: 21706094 
• DOI: https://doi.org/10.1039/c1cc10345h
• Primary Citation Related Structures: 
  3PYK


• PubMed Abstract: 
  

  d(6)-piano-stool complexes bearing an arylsulfonamide anchor display sub-micromolar affinity towards human Carbonic Anhydrase II (hCA II). The 1.3 Å resolution X-ray crystal structure of [(η(6)-C(6)Me(6))Ru(bispy 3)Cl](+)⊂ hCA II highlights the nature of the host-guest interactions.

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Organizational Affiliation: 
• Department of Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.32 kDa 
• Atom Count: 2,594 
• Modeled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 1  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRX	C [auth A]	chloro{N-[di(pyridin-2-yl-kappaN)methyl]-4-sulfamoylbenzamide}[(1,2,3,4,5,6-eta)-(1R,2R,3R,4S,5S,6S)-1,2,3,4,5,6-hexamethylcyclohexane-1,2,3,4,5,6-hexayl]ruthenium(2+) C30 H34 Cl N4 O3 Ru S QUFOPYMQVADRIK-UHFFFAOYSA-M
MMC	D [auth A]	METHYL MERCURY ION C H3 Hg DBUXSCUEGJMZAE-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.165 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.099	α = 90
b = 41.493	β = 104.33
c = 72.382	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Heinisch, T., Schirmer, T.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2011-07-27
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description